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Wrestling Resistance

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To improve the detection and treatment of drug-resistant pathogens, researchers in academia and industry are collaborating to develop the ideal microbiology sequencing platform for the clinic.

The European Union has awarded around $2.9 million to Oxford Gene Technology to fund a three-year project called PATHSEEK, which aims to refine enrichment methods for clinical microbiology labs and speed up the time it takes for clinical sequencing platforms to provide data on mutations associated with drug resistance. The team also plans to explore how next-generation sequencing can be used to help combat drug-resistant pathogens in the clinic and to establish connections among infections from different patients.

"There are quite a lot of pathogens for which drug resistance is not possible to easily test ... such as Chlamydia [trachomatis], which is hard to grow and takes a long time to culture, making it hard to work out their drug resistance quickly," says University College London's Judy Breuer, who is leading the effort. "This methodology, if it works, will allow us to sequence the pathogens very quickly and determine the drug resistance in a clinically relevant time frame."

Beyond chlamydia, PATHSEEK will also focus on a number of other infectious diseases, including hepatitis, HIV, tuberculosis, and the flu.

Next-generation sequencing technologies allow researchers to quickly sift through whole bacterial and viral genomes, in which drug resistance-associated genes are often widely dispersed.

"You can look at the minority of variants within the sequencing reaction and actually determine if there are minority sequences that are contributing to a resistance phenotype," she says. "Or, if there is an emergence over time, [you can] look at the increasing frequency of a mutation, so you can actually change drugs before resistance takes over completely."

Breuer says that her team hopes its sequencing and informatics platform will provide clinicians with a streamlined alternative to some of the more time-consuming methods currently used in microbiology labs, such as PCR or culturing.

"We aim to produce a turnaround of 24 to 48 hours, and part of the project is to work out which sequencing platform will give us the best turnaround time and also to couple that to the targeted enrichment methods," she says.

As with many applications of next-generation sequencing, the challenges of data management and analysis will have to be dealt with effectively — especially if the idea is to produce a platform that will work seamlessly at the bedside. To ensure that the technology developed during the PATHSEEK project is paired with an informatics solution that is specifically tailored for drug resistance detection in the clinic, the researchers will also harness the bioinformatics expertise of Danish software vendor CLC Bio.

"The idea will be to develop simple tools to allow people to interpret the data pretty quickly and automatically, and to use it clinically," Breuer adds.

In addition to delivering a proof-of-concept solution for detecting drug resistance in a single sample, Breuer says she hopes the PATHSEEK platform will also allow users to easily relate different pathogens to each other to determine whether there has been a transmission of the pathogen among individuals.

"If you have the sequence data, you can look at that together with phylogenetic analysis and determine if there has been a transmission event or outbreak [that] has not yet been detected and use it for public health purposes as well," she says. "The information will have two applications really."

Ultimately, she adds, the focus is on how these components might be combined into an efficient — and affordable — platform for detecting drug resistance in pathogens from a single clinical sample.

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